BN0415 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 2 5.8249e-07 3.8492e-03
Layer 3 3.3360e-06 2.4889e-04
Layer 4 3.9781e-06 1.4020e-04
Layer 5 3.8025e-05 1.3245e-03
Layer 6 2.7067e-04 3.9313e-03
WM 4.1220e-02 1.9846e-01
Layer 1 3.7431e-01 4.1315e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
CHGA Expression Distribution
Gene Specificity Score (GSS)
CHGA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
CHGA Layer 4 2.8594 0.7676
INA Layer 4 2.9414 0.7460
SERPINI1 Layer 4 2.3398 0.7431
GABRG2 Layer 4 2.8281 0.7430
CALY Layer 3 2.3965 0.7429
EPHA4 Layer 4 2.8457 0.7418
INPP5F Layer 4 2.7070 0.7410
SLC12A5 Layer 4 2.5566 0.7390
MEF2C Layer 4 2.6543 0.7375
ELAVL4 Layer 4 2.9531 0.7367
ATP6V1B2 Layer 4 2.4082 0.7325
NSF Layer 4 2.4570 0.7309
SNAP91 Layer 4 2.5566 0.7297
BLCAP Layer 4 2.6133 0.7273
TOLLIP Layer 3 2.3398 0.7226
STX1B Layer 4 2.7070 0.7204
AUXG01000058.1 Layer 3 2.8223 0.7199
SIRPA Layer 4 2.3867 0.7188
NRXN1 Layer 3 2.5840 0.7185
NEFM Layer 3 3.0449 0.7177
PNMA2 Layer 4 2.6484 0.7166
GUCY1B1 Layer 4 2.4844 0.7163
GABRB2 Layer 3 2.7070 0.7160
EPB41L1 Layer 4 2.5664 0.7159
NPTN Layer 4 2.5059 0.7135
TMX4 Layer 4 2.4395 0.7122
CEND1 Layer 4 2.4844 0.7102
SYT13 Layer 3 2.6309 0.7097
SNCG Layer 3 3.1602 0.7078
ATP1A3 Layer 4 2.4238 0.7071
SLC9A6 Layer 4 2.4512 0.7068
KCNA2 Layer 3 2.5273 0.7062
CAMK2G Layer 3 2.3184 0.7061
OPTN Layer 3 2.1777 0.7058
CTBP1 Layer 3 2.3086 0.7049
NDRG4 Layer 5 2.2773 0.7046
ATP2B2 Layer 3 2.7656 0.7043
YPEL3 Layer 4 2.2832 0.7031
SNCB Layer 4 2.5059 0.7021
OIP5-AS1 Layer 4 2.5332 0.7019
PREPL Layer 4 2.4023 0.7014
SULT4A1 Layer 4 2.8457 0.7011
SCN1B Layer 4 3.6133 0.7007
TUBB4B Layer 4 2.5332 0.7007
GPI Layer 4 2.5117 0.7006
DIRAS1 Layer 4 2.6309 0.7003
SYNGR3 Layer 4 2.5898 0.7003
RAB3A Layer 6 2.4512 0.6998
ATP5F1A Layer 4 2.5176 0.6993
PNMA8A Layer 4 2.5176 0.6992

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0415
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0415_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0415/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0415/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0415/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0415/report/PD/BN0415_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0415/report/PD/BN0415_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 00:04:01
  • Number of Processes: 10
  • Spending Time: 0h 4m